/**
 * PHOSIDE: PHosphorylation Site IDentification Engine.
 * Copyright 2009 Digital Biology Lab, University of Missouri.
 * This library is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License as published by the Free Software
 * Foundation; either version 3 of the License, or (at your option) any later
 * version. <p/> This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the License for more
 * details.
 */

package phoside.util;

import phoside.io.fasta.parser.HeaderRule;
import phoside.io.fasta.parser.DefaultHeaderRule;

/**
 *
 * @author gjj
 */
public class StaticFinalValues {
    public static final String ACCESSION = "accession";
    public static final String DESCRIPTION = "description";
    public static final String SYMBOL = "symbol";
    public static final String SPECIES = "species";
    public static final String SITES = "sites";
    public static final String SEQUENCE = "sequence";
//    public static final String KINASE = "kinase";
    public static final String SITENOTES = "site_notes";
    public static final String PREDICTION = "predicted-score";
    public static final String QUERY = "query";

    public static final String SEPARATOR = "; ";

    public static final String DISORDER = "disorder";
    public static final String AAFREQUENCY = "aafrequency";
    public static final String KNN = "knn";

    public static final String INSTANCETAGNAMEPROTEIN = "tag_protein";
    public static final String INSTANCETAGNAMESITE = "tag_site";

    public static final String TMPDIR = "tmp";

    public static final String RESOURCEDIR = "resource";

    public static final String MATRIX = "matrix";
    
    public static final String MODELAPPEDIX = "model";

    public static final String MODELDIR = "model";

    public static final String THIRDPARTYDIR = "3rd_party";

    public static final String DISORDERAPPENIX = "disorder";

    public static final String DEFAULTACCREGEX = "(.+)";
    public static final HeaderRule DEFAULTHEADERRULE = new DefaultHeaderRule(DEFAULTACCREGEX);

    public static final String PROPSDIR = "props";

    public static final String GLOBALPROPSFILE = "phoside.param";

    // Global parameter
    public static final String SVMTRAINDIR = "SVM train program";
    public static final String SVMCLASSIFYDIR = "SVM classify program";
    public static final String DISORDERPREDICTORVSL2 = "Disorder predictor";
    public static final String BLASTCLUSTER = "BLASTClust";

    public static final String TRAININGPROPSFILE = "training.param";
    
    // training parameter
    public static final String SVMPARAMETERS = "SVM parameters";

    public static final String NOOFBOOTS = "No. of boots for positive/negative set";
    public static final String NOOFCLASSIFIERS = "No. of classifiers aggregated";

    public static final String NEGATIVECONTROLSIZE = "Number of negative data for specificity estimation";

    public static final String USEKNNFEATURES = "KNN features to be used?";
    public static final String SUBSTITUTIONMATRIX = "KNN substitution matrix";
    public static final String KNNWINDOWSIZE = "KNN window sizes";
    public static final String KNNNEIGHBORSIZES = "KNN neighbor sizes (% of bootstrapped sample)";

    public static final String USEDISORDERFEATURES = "Disorder features to be used";
    public static final String DISORDERWINDOWSIZES = "Disorder window sizes";

    public static final String USEFREQUENCYFEATURES = "Frequency features to be used";
    public static final String FREQUENCYWINDOWSIZE = "Frequency window size";
    public static final String FREQUENCYFEATURENUMBER = "Frequency feature number";

    public static final String PADDINGTERMINALS = "Padding terminals";

//    public static final Map<String,String> PARAM_DISPLAY_NAME;
//    static {
//        PARAM_DISPLAY_NAME = new HashMap();
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(, );
//        PARAM_DISPLAY_NAME.put(DISORDERWINDOWSIZES, "Window sizes for disorder features");
//        PARAM_DISPLAY_NAME.put(USEFREQUENCYFEATURES, "Use frequency features when training?");
//        PARAM_DISPLAY_NAME.put(FREQUENCYWINDOWSIZE, "Window size of frequency features");
//        PARAM_DISPLAY_NAME.put(FREQUENCYFEATURENUMBER, "Number of frequency features");
//        PARAM_DISPLAY_NAME.put(PADDINGTERMINALS, "Padding terminals?");
//
//    }

}
